I had many applications show up as "Installed" in the update pane of the Mac App Store even after I had updated them. Apparently, if you have copies of an application on your system, even on a secondary drive, they are discovered by the Mac App Store. This causes a problem if you have a copy an application in the /Applications directory as well as somewhere else on your drive. If you update the application in the /Applications directory but not the other instance then the Mac App store will display the application on the Update Pane, but list it as "installed". Simply deleting the other instance of the application will cause the Mac App Store to refresh it's data and remove the application from the update list.

[kirkmc adds: I was seeing that in the early days of Mountain Lion. After running the updates again, they disappeared; I didn't think to check my backup drive, were I clone my startup volume, to see if those copies of my apps got updated.

I just checked the Mac App Store and found two updates waiting for me. (I thought it was supposed to alert me when there were updates?) I updated one app, quit the Mac App Store, then re-launched it; that app was no longer listed. So this may be a transient problem that Apple has resolved, but I'm publishing it anyway, in case others still see this issue.]

This doesn't seem to address all possible situations in which you've got a zombie app in the MAS... I've had one showing up in there as needing an update for over a month (started under 10.7.4, continues under 10.8). Zero other copies on any connected drives, and receipts removed; still showing up.

Now, I *do* have a Time Capsule backup where another copy of the app is probably located, but it's only mounted while it's backing up. Also, there will be all *sorts* of old MAS apps in there that I have since deleted from my main drive, but none of those are showing up in the store — something's wrong with this one app.

BTW, I have had the Windows Phone 7 Connector showing up as updatable in the MAS for months, now, on all of my Macs; and updating or reinstalling it changes nothing: it still shows up with an "Update" instead of "Installed" description, on the right side of the "Purchased" part of the MAS window (it isn't explicitly offered as an update, however, also because there's currently no update available for this application).

I also had this problem of zombie apps in the mac app store, because it was also seeing the app on my back drives.

I just fixed this by going into Sys Prefs > Spotlight > Privacy and adding my backup drive to this list. Literally as soon as the drive appeared in this list the updates list in MAS showed "No Updates Available".